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PubMed1976

Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes.

The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA from Bacillus subtilis, B. firmus, B. pasteurii, B. brevis, Lactobacillus brevis and Streptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided for B. cereus and Sporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.

Bacillus↗
PubMed1998

Creating and curating a pediatric radiology digital library to make the internet a useful reference tool for the radiologist.

BACKGROUND: To practice pediatric radiology optimally, radiologists need convenient access to organized and authoritative pediatric radiology information. The Internet has the potential for offering such convenient access, but the majority of information on it is poorly organized and of questionable authority. OBJECTIVE: The goal of this project was to create and curate a pediatric radiology digital library that will make the Internet a useful reference tool for the radiologist at the point-of-care. MATERIALS AND METHODS: A pediatric radiology digital library containing organized and authoritative pediatric radiology information from the Internet was created and has three components : (1) PediatricRadiology.com (http://pediatricradiology.com)--a catalog of pediatric radiology Web sites; (2) The MetaTextbook of Pediatric Radiology (http://www. vh.org/Providers/TeachingFiles/MetatextbookPedRad/MetaTBP edRad.html)--a catalog of pediatric radiology teaching file cases on the Internet; and (3) Paediapedia (http://www.vh. org/Providers/TeachingFiles/PAP/PAPHome.html)--an imaging encyclopedia of pediatric disease. The pediatric radiology digital library is curated regularly. RESULTS: Over 7 months, 223,689 pages of information were read and 26,972 images were viewed in the pediatric radiology digital library by 69,866 individual users, with 20% of the users from outside the United States. CONCLUSION: Creating a pediatric radiology digital library that identifies and organizes authoritative pediatric radiology information and makes it conveniently available can allow radiologists to use the Internet productively as a reference tool.

Child↗
PubMed2005

A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

Animals↗
PubMed1990

Database management for a gynecologic oncology service.

With the ready availability of powerful desktop computers, the ability to manage large clinical databases has become practical. A computer can enhance the capability of a gynecologic oncology service to catalog, recall, and analyze data about patients, tumors, and therapies. While commercially available database packages can be used for this purpose, we have developed a custom database for tracking the clinical activity of a busy gynecologic oncology service. The system catalogs data about patients, admissions, tumors, and therapeutic modalities and uses this information to generate several useful reports. The reports are used for daily patient care, fellow and resident case statistics, and clinical research. What is unique about the system is that it is optimized for ease of use. The development of this tumor registry, its user friendliness, and advantages over a manual recordkeeping system are described. Unlike other tumor registries, our system is utilized on a daily basis for patient care. Therefore, the data being entered have an immediate usefulness in addition to being simultaneously added to the tumor register for retrospective clinical research. One may hypothesize that it would be useful if all gynecologic oncology services used a common computerized tumor registry that could allow for the sharing of information on a national or global scale.

Database Management Systems↗
PubMed2026

Genomic and biosynthetic landscape of high-temperature Daqu microbiome.

As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82 % of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3 % are novel, and 17,031 biosynthetic gene clusters, of which 62.63 % are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.

Microbiota↗
PubMed2025

A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.

The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.

Lakes↗
PubMed2026

Chromosome-scale genome remodeling in tumor evolution: Copy number alterations and structural variants as two sides of the same coin.

Chromosome-scale genomic rearrangements are a dominant force in tumor evolution. Copy-number alterations (CNAs) and structural variants (SVs) constitute two complementary axes of this process. Although detection technologies now deliver near-comprehensive catalogs, technical resolution has outpaced conceptual integration. In this review, we frame CNAs and SVs as inextricable facets of chromosomal aberrations. They reshape cancer genomes through altered gene dosage and three-dimensional regulatory rewiring. CNAs quantify the gene-dosage imbalance, yet arise through mechanistically distinct routes. Segmental CNAs typically require chromosomal breakage, and therefore often coincide with SV junctions. By contrast, whole-chromosome aneuploidy and whole-genome doubling (WGD) primarily reflect mitotic or cytokinetic failure and can occur without local breakpoints, while nevertheless reshaping the karyotypic landscape and seeding subsequent structural complexity. SVs, in turn, range from unbalanced events that alter copy number to ostensibly balanced exchanges that predominantly rewire regulatory architecture. Despite their diverse and sometimes catastrophic architectures, SVs are ultimately rooted in double-strand break formation and error-prone resolution. By integrating CNAs and SVs within a unified mechanistic and functional framework, we aim to convert catalogs into concepts and distill the organizing principles that govern tumor genome evolution.

Humans↗
PubMed2005

Status of activator methods chiropractic technique, theory, and practice.

OBJECTIVE: To provide an historical overview, description, synthesis, and critique of the Activator Adjusting Instrument (AAI) and Activator Methods Chiropractic Technique of clinical assessment. METHODS: Online resources were searched including Index to Chiropractic Literature, EBSCO Online, MANTIS, CHIROLARS, CINAHL, eJournals, Ovid, MDConsult, Lane Catalog, SU Catalog, and Pubmed. Relevant peer-reviewed studies, commentaries, and reviews were selected. Studies fell into 2 major content areas: instrument adjusting and the analysis system for therapy application. Studies were categorized by research content type: biomechanical, neurophysiological, and clinical. Each study was reviewed in terms of contribution to knowledge and critiqued with regard to quality. DISCUSSION: More than 100 studies related to the AAI and the technique were found, including studies on the instrument's mechanical effects, and a few studies on clinical efficacy. With regard to the analysis, there is evidence for good reliability on prone leg-length assessment, but to date, there is only 1 study evaluating the Activator Methods Chiropractic Technique analysis. CONCLUSION: A body of basic science and clinical research has been generated on the AAI since its first peer-reviewed publication in 1986. The Activator analysis may be a clinically useful tool, but its ultimate scientific validation requires testing using sophisticated research models in the areas of neurophysiology, biomechanics, and statistical analysis.

Clinical Trials as Topic↗
PubMed2006

The S. purpuratus genome: a comparative perspective.

The predicted gene models derived from the sea urchin genome were compared to the gene catalogs derived from other completed genomes. The models were categorized by their best match to conserved protein domains. Identification of potential orthologs and assignment of sea urchin gene models to groups of homologous genes was accomplished by BLAST alignment and through the use of a clustering algorithm. For the first time, an overview of the sea urchin genetic toolkit emerges and by extension a more precise view of the features shared among the gene catalogs that characterize the super-clades of animals: metazoans, bilaterians, chordate and non-chordate deuterostomes, ecdysozoan and lophotrochozoan protostomes. About one third of the 40 most prevalent domains in the sea urchin gene models are not as abundant in the other genomes and thus constitute expansions that are specific at least to sea urchins if not to all echinoderms. A number of homologous groups of genes previously restricted to vertebrates have sea urchin representatives thus expanding the deuterostome complement. Obversely, the absence of representatives in the sea urchin confirms a number of chordate specific inventions. The specific complement of genes in the sea urchin genome results largely from minor expansions and contractions of existing families already found in the common metazoan "toolkit" of genes. However, several striking expansions shed light on how the sea urchin lives and develops.

Animals↗
PubMed1998

Bioinformatics: searching the Net.

During the past 30 years, there has been an explosion in the volume of published medical information. As this volume has increased, so has the need for efficient methods for searching the data. MEDLINE, the primary medical database, is currently limited to abstracts of the medical literature. MEDLINE searches use AND/OR/NOT logical searching for keywords that have been assigned to each article and for textwords included in article abstracts. Recently, the complete text of some scientific journals, including figures and tables, has become accessible electronically. Keyword and textword searches can provide an overwhelming number of results. Search engines that use phrase searching, or searches that limit the number of words between two finds, improve the precision of search engines. The development of the Internet as a vehicle for worldwide communication, and the emergence of the World Wide Web (WWW) as a common vehicle for communication have made instantaneous access to much of the entire body of medical information an exciting possibility. There is more than one way to search the WWW for information. At the present time, two broad strategies have emerged for cataloging the WWW: directories and search engines. These allow more efficient searching of the WWW. Directories catalog WWW information by creating categories and subcategories of information and then publishing pointers to information within the category listings. Directories are analogous to yellow pages of the phone book. Search engines make no attempt to categorize information. They automatically scour the WWW looking for words and then automatically create an index of those words. When a specific search engine is used, its index is searched for a particular word. Usually, search engines are nonspecific and produce voluminous results. Use of AND/OR/NOT and "near" and "adjacent" search refinements greatly improve the results of a search. Search engines that limit their scope to specific sites, and metasearch sites that use multiple search engines optimized for specific types of searches have recently emerged. The distinctions between search engines and directory searches have blurred. Eventually, conceptual searching in which the computer searches for related ideas, without having to be given all the related keywords, may become a reality. This will free the user from having to learn specific rules about searching, allowing energies to be focused on results of the search, not the search itself.

Computational Biology↗
PubMed1997

Influences on the selection of dietetics as a career.

OBJECTIVE: To gather information on the factors that influence students' decisions to choose dietetics as a career. DESIGN: Self-administered questionnaires regarding the point at which career decisions were made were completed by 1,695 students in Plan IV/V dietetics programs throughout the United States. SUBJECTS: All Plan IV/V dietetics programs that reported greater than five graduates in the academic year 1989 to 1990 were selected from the 1990-1991 Directory of Dietetic Programs for the sample population. Of the 156 schools that were mailed questionnaires, responses were received from 84 schools (54%). Almost 90% of the students were women, 10.6% were men. STATISTICAL ANALYSES: Data were analyzed using the Statistical Package for the Social Sciences. A chi 2 analysis was used to examine the relationship between point of decision and factors that influenced career choice, including people who influence career choice. RESULTS: The majority of students (55%) questioned reported making their career decision in college. Students rated interest in nutrition (96.3%) and job enjoyment (93.8%) as factors that were important in their decision to pursue a career in dietetics. College catalogs were rated by 48.3% of the students as being either useful or very useful in helping them make their career selection. With respect to gender differences, women rated a diverse work environment as being very important to their career decision more frequently than men (chi 2 = 15.44, P < .01). Women were more likely than men to rate part-time work opportunities as being very important (chi 2 = 26.75, P < .001); and selected working with people as being very important to their career decision (chi 2 = 17.59, P < .01). CONCLUSIONS: Findings identified that recruitment strategies need to be audience specific. Because career decision making appears to occur during one of three time frames (high school, college, or work experience), recruitment activities should be developed to specifically target students at these times. One way to increase the exposure of students to the profession of dietetics is for registered dietitians to give guest lectures in introductory college courses and high school upper-class courses in health, home economics, and biology. The use of university/college catalogs as effective marketing tools should also not be underestimated. Data suggest that gender differences exist in factors that influence persons to choose dietetics as a career. To increase the number of men who pursue careers in dietetics, future research should be designed to more fully explore gender differences, so that strategies to recruit more men into the profession can be developed.

Adolescent↗
PubMed1996

Chronic prostatitis: results of an Internet survey.

OBJECTIVES: Chronic prostatitis is a common diagnosis, but the etiology of this disease is unknown. We sought to catalog symptoms and etiologic factors for chronic prostatitis to gather epidemiologic data about the disease. We also sought to determine the feasibility of doing this using the Internet. METHODS: A 54-questions survey was designed and posted to several Internet newsgroups dealing with chronic prostatitis. The questions dealt with symptoms, predisposing factors, demographic data, and sexual practices. Responses were collected by electronic mail and tabulated at a central site. RESULTS: We received 163 completed surveys over a 2-month period. Nine percent of responses came from individuals outside the United States or Canada. Only 9.8% of complete surveys contained one or more unreadable answers. The responding population consisted of relatively young men (mean age 43 years) with a chronic, relapsing set of symptoms mostly characterized by pain at various locations in the pelvis, irritative voiding symptoms, and pain associated with ejaculation. Most respondents were potent and had a single sexual partner. CONCLUSIONS: This catalog of symptoms will be useful in the design of a standardized instrument to distinguish the population of men with prostatitis from normal men or men with benign prostatic hyperplasia. The facility of conducting patient surveys by Internet is demonstrated.

Adult↗
PubMed1984

The phylogenetic relationships of three sulfur dependent archaebacteria.

Oligonucleotide catalogs have been determined for the 16S ribosomal RNAs of three sulfur dependent (i.e. "thermoacidophilic") archaebacteria--Sulfolobus acidocaldarius, S. solfataricus, and Thermoproteus tenax. The three form a group specifically related to one another, but are only distantly related to the other archaebacteria--i.e. the group comprising the methanogens, extreme halophiles, and (peripherially) the genus Thermoplasma. The three catalogs exhibit two features unique among bacteria: (1) an unusually high number of long pyrimidine runs, and (2) a remarkably high number of (post-transcriptionally) modified nucleotides.

Archaea↗
PubMed1986

Characteristic archaebacterial 16S rRNA oligonucleotides.

A method of analyzing 16S rRNA catalog data has been developed in which groupings at various taxonomic levels can be characterized in terms of specific "signature" oligonucleotides. This approach provides an alternative means for evaluating higher order branching possibilities and can be used to assess the phylogenetic position of isolates that are poorly placed by the usual clustering procedures. This signature approach has been applied to forty archaebacterial catalogs and every oligonucleotide with significant signature value has been identified. Sets of specific oligonucleotides were identified for every major group on a dendrogram produced by cluster analysis procedures. Signatures that would establish between group relationships were also sought and found. In the case of the Methanobacteriaceae the clustering methods suggest a specific relationship to the Methanococcaceae. This inclusion is in fact supported by six strong signature oligonucleotides. However there are also significant numbers of signature oligonucleotides supporting a specific relationship of the Methanobacteriaceae to either the Halobacteriaceae or the Methanomicrobiaceae. Thus the placement of the Methanobacteriaceae is less certain than the usual dendrograms imply. The signature approach also was used to assess the phylogenetic position of Thermoplasma acidophilum which is found to be more closely related to the methanogen/halophile Division than to the sulfur dependent Division of the archaebacteria. This does not imply however that Thermoplasma acidophilum is properly regarded as being in the methanogen/halophile Division.

Archaea↗
PubMed1988

Calcified aortic sinotubular ridge: a source of coronary ostial stenosis or embolism.

This report reviews the findings in a calcified lesion involving the ridge at the junction of the sinus and tubular portions of the ascending aorta. The histologic features resemble the alterations in calcified aortic valve and do not exhibit those of atherosclerosis. The 37 cataloged cases are among the more severe and dramatic instances of a lesion more common than the cataloged number would suggest. The involved ridge may be related to any of the sinuses, although that related to the right aortic sinus is most commonly affected. Major complications include coronary ostial stenosis or embolism in an epicardial coronary artery. Ostial stenosis results either from overhanging of an ostium by the aortic lesion or from invasion of the wall of the aorta at the site of the arterial takeoff.

Age Factors↗
PubMed2026

Genome-Resolved Metagenomics Revealed the Functional Potential of Core Novel and Known Genera Key to Processes in Full-Scale Aerobic Granular Sludge Plants.

Microbial communities are critical for nutrient removal in aerobic granular sludge (AGS) wastewater treatment plants (WWTPs). Despite the stable long-term operation of full-scale AGS WWTPs, the microbial populations and functional traits sustaining stable long-term performance remain poorly resolved. To address this gap, the recovered MAG catalog from nine full-scale AGS WWTPs across five countries was analyzed. From this catalog, 74 high-quality core MAGs were identified and used for downstream taxonomic characterization and functional analyses. These high-quality core MAGs spanned 48 established and 7 novel genera, representing 31 known and 43 novel species. Functional analysis linked core MAGs to key WWTP processes: polyphosphate accumulation (9), glycogen accumulation (12), denitrification (62), and nitrification (1). These included four novel MAGs with glycogen-accumulating (3) and polyphosphate-accumulating (1) potential and 11 capable of nitrous oxide reduction, critical for mitigating greenhouse gas emissions. Ca. Phosphoribacter was the most abundant genus, highlighting its underestimated role caused by misclassification as Tetrasphaera in 16S rRNA surveys. Specifically, Ca. P. hodrii was the dominant species, exhibiting enhanced sugar uptake and amino acid synthesis as likely drivers of its enrichment in the AGS WWTPs. Overall, this study resolves for the first time the taxa and functional traits consistently enriched in full-scale AGS systems, enabling a shift from an empirical performance assessment toward biologically informed process interpretation.

Sewage↗
PubMed2006

Characterization of the human salivary proteome by capillary isoelectric focusing/nanoreversed-phase liquid chromatography coupled with ESI-tandem MS.

Saliva is a readily available body fluid with great diagnostic potential. The foundation for saliva-based diagnostics, however, is the development of a complete catalog of secreted and "leaked" proteins detectable in saliva. By employing a capillary isoelectric focusing-based multidimensional separation platform coupled with electrospray ionization tandem mass spectrometry (MS), a total of 5338 distinct peptides were sequenced, leading to the identification of 1381 distinct proteins. A search of bacterial protein sequences also identified many peptides unique to several organisms and unique to the NCBI nonredundant database. To the best of our knowledge, this proteome study represents the largest catalog of proteins measured from a single saliva sample to date. Data analysis was performed on individual MS/MS spectra using the highly specific peptide identification algorithm, OMSSA. Searches were conducted against a decoyed SwissProt human database to control the false-positive rate at 1%. Furthermore, the well-curated SwissProt sequences represent perhaps the least redundant human protein sequence database (12,484 records versus the 50,009 records found in the International Protein Index human database), therefore minimizing multiple protein inferences from single peptides. This combined bioanalytical and bioinformatic approach has established a solid foundation for building up the human salivary proteome for the realization of the diagnostic potential of saliva.

Chromatography, Liquid↗
PubMed2007

Tissue-specific regulatory elements in mammalian promoters.

Transcription factor-binding sites and the cis-regulatory modules they compose are central determinants of gene expression. We previously showed that binding site motifs and modules in proximal promoters can be used to predict a significant portion of mammalian tissue-specific transcription. Here, we report on a systematic analysis of promoters controlling tissue-specific expression in heart, kidney, liver, pancreas, skeletal muscle, testis and CD4 T cells, for both human and mouse. We integrated multiple sources of expression data to compile sets of transcripts with strong evidence for tissue-specific regulation. The analysis of the promoters corresponding to these sets produced a catalog of predicted tissue-specific motifs and modules, and cis-regulatory elements. Predicted regulatory interactions are supported by statistical evidence, and provide a foundation for targeted experiments that will improve our understanding of tissue-specific regulatory networks. In a broader context, methods used to construct the catalog provide a model for the analysis of genomic regions that regulate differentially expressed genes.

Algorithms↗